Because in computers, everything is done from the top left to the bottom right. I could have made my program use Cartesian coordinates and then translate them to the inverted y axis system every time I want to render it on the screen, but I chose not to.

Now, about the inverting. My suggestion is invert the polar angle as well. Instead of counterclockwise being positive, make clockwise positive.
This way the conversion formula is exactly the same as the normal polar to rectangular.